Post on 17-Apr-2018
Molecular Graphics What?
PDF-4 products contain data sets with atomic coordinates.
Two molecular graphic packages embedded in the product
allows molecules to be displayed (above). Data can also be
exported for use in other graphics utility programs.
PDF 00-057-0248
ULM-8
A microporous
florinated gallium
phosphate with
N4C6H19 in the
pores
Molecular Graphics Why?
Through the use of molecular graphics, molecules can be visualized
and examined for their conformation. This is important in
understanding how materials react and interact.
The particular molecular graphics package employed in PDF-4 was
originally developed by a team at Crystal Impact, as part of the Linus
Pauling Project, headed by Dr. Pierre Villars, President of Material
Phases Data System (MPDS). This package also examines the
“atomic environment” around each atom as a means of studying
molecular “building blocks” and determining structural prototypes.
This graphic package is explained in this tutorial.
In PDF-4 Release 2011, a second graphics package was added
called Jmol (www.jmol.org). This package can plot multiple unit cells,
autorotate the molecules, and express the molecules as polyhedra.
This graphics package is explained in the tutorial “Use 3D Structure
Capabilities”.
Molecular Graphics How?
Symmetry Operators
Atomic Coordinates
Symmetry
Wyckoff Notation
Atom Designations
Temperature
Factors
ITF = Isotropic
(shown)
Table provided
for anisotropic
factors
Site Occupancy
Factor (SOF)
Molecular graphics are calculated from
the atomic parameters and symmetry
operators shown in the Structure tab of a
PDF Card. The unit cell parameters in the
Crystal tab are also used.
PDF 04-007-8587, Cryolite
Cross References
Some entries, especially those from powder data, may not have atomic coordinates
under the Structure Tab. In the Miscellaneous Tab of every entry, cross references where
the formula and unit cells match the entry, are listed. The entries with atomic coordinates
are listed with a check mark. To find the appropriate set of atomic coordinates just
double click on the entry number.
Getting Started To display molecules and atomic environments, you need to have atomic
parameters, space groups and a unit cell. Space groups and unit cells are
published for most data in the PDF. In PDF-4+, Web PDF-4 and PDF-
4/Minerals the majority of entries have atomic coordinates or cross
referenced atomic coordinates. In PDF-4/Organics >30,000 entries have
atomic coordinates.
Data Sources for the PDF
Coordinates in
Source of Data the PDF-4 Reference*
LPF Yes, All Data Yes
ICSD Select data Yes
CSD Select data Yes
ICDD Select data Yes
NIST Majority Yes
* All references contain both a reference to the single
crystal source data (ICSD, NIST, CSD, LPF) and a primary
literature reference.
PDF-4+ contains over
200,000 entries with
atomic coordinate sets or
direct cross references to
atomic coordinate sets.
Finding Entries with Atomic Coordinates
Go to the main
Search page
Click Search
on the toolbar Click on the
Structure tab
Use the
“Has Atomic
Coordinates”
search
This search can be
combined with any
other search.
A search of zeolites having atomic
coordinates finds 436 entries.
Finding Entries with Atomic Coordinates
Finding Entries with Atomic Coordinates
In recent years, the box on the left has been replaced with the box on
the right. In PDF-4+, the >160,000 entries with atomic coordinates are
supplemented by another >40,000 entries with cross references.
Molecular Graphics From an Entry
From the previous search
we selected Zeolite A, PDF
04-010-2030.
The tool bar at the top of the
entry contains several graphics
options.
Selecting results in the
molecular graphic menus.
Selection of the Graphics Program The automatic molecular graphics default program is Jmol. To select another
program, click the preferences menu on any entry.
Then select ICDD or Jmol
3D Structure Viewer from the
drop down menu.
Display Options thumbnails – in the product, double click for full scale
The Display options include:
1) unit cell – top row left
2) 2D cell projections – top row
3) atomic environments – middle and
bottom row
Rotate
x, y or z
Change atom colors
Replace atom
labels with
Wyckoff labels
and color codes
Zeolite A – Different viewing options
Export and Import
This rotating display was made
by exporting molecular graphics,
taken at various rotation angles
(shown in the previous slides),
and importing the data into
Adobe® Photoshop®.
Distributor Software
ICDD works with software distributors of many of the worlds’ molecular
graphics programs to provide enhanced molecular displays.
The distributors work with data tables of atomic coordinates, unit cell
parameters, temperature factors, space groups and symmetry
operators contained within the PDF-4 so that data are automatically
entered into their molecular display programs.
The ICDD also works with many software developers and instrument
manufacturers who produce molecular refinement programs (i.e.,
Rietveld Analyses). These programs export atomic coordinates
for both refinement and molecular display.
In general, these programs offer tremendous convenience and speed
since the user does not have to provide export/import.
xml Files
In the xml “card” format, all data
are exported. This includes
formula, nomenclature, atomic
coordinates, anisotropic
temperature factors, references,
comments, etc., as shown in the
boxes on the left.
It also displays a fully indexed
diffraction pattern (not shown).
How to Export – CIF, JPG, CSV Files
Same Zeolite A entry
displayed on earlier slides.
Go to the Toolbar
Click on Diffraction Pattern
How to Export – CIF, JPG, CSV Files
The program will calculate and display
a digital diffraction pattern. This pattern
with atomic parameters and unit cell data
can be saved to an export file.
In this example, we are exporting the data in a CIF (2 theta, I) format.
The CIF format is used by a wide variety of software programs.
Export/Import
The next three slides are meant to demonstrate how PDF-4+ data
can be imported into common molecular visualization programs.
The programs selected are the proprietary software products
of ICDD’s database partners. Examples are shown to display
a few select capabilities, each program has a large number of
display options.
Program
Cambridge Crystallographic
Data Centre (CCDC) Mercury
Fachinformationszentrum
Karlsruhe (FIZ) Visualize
Material Phases Pearson’s Crystal Data
Data System
http://www.ccdc.cam.ac.uk/products/mercury
Importing CIF Files PDF-4+ data file imported into Mercury. Mercury is a freeware program
produced by the CCDC, and used with the CSD.
Wireframe
Ball and Stick Packing
Multiple Unit Cells Zeolite A
Importing CIF files PDF-4+ data file imported into Visualize. Visualize is a program
produced by FIZ/NIST for the ICSD.
Space Fill Model
VRML Model
Zeolite A
Same Structure Viewed with Pearson’s Crystal Data
Molecular Visualization Software Note: This uses the PDF-4+ cross reference.
Wireframe
All Wire
Space
Filling
Editing and Molecular Visualization
Historically, many databases have faced issues displaying
molecular structures. The primary issue has been the lack of
uniform conventions and the back-application of recent conventions
to historic data.
ICDD Editors:
Standardize all unit cell settings
Convert non-standard space groups
Check and test that the appropriate temperature
factors are applied from the literature
Analyze for correct bond angles and distance
Check for non-positive temperature factors
Ensure that the physical properties match the stated
chemistry and crystallography
Apply a quality evaluation system to all entries,
including historic data, and publish the results in
the comment sections of each entry.
International Centre for Diffraction Data
12 Campus Boulevard
Newtown Square, PA 19073
Phone: 610.325.9814
Toll Free Number in US & Canada: 866.378.0331
Fax: 610.325.9823
Thank you for viewing our tutorial.
Additional tutorials are available at the ICDD web site (www.icdd.com).